Can I change the color of the last selected face?
Yes.

In CtrlAltU> User preferences > Themes > 3D view:




The Face Selected color controls the color of the selected face
The Active Vert/Edge/Face color controls the color of the last selected face.


However, I wouldn't recommend making these colors too similar, as there are differences between the selected faces and the last selected face (active) and it might be confusing if you can't tell if a face is active or selected.

Reducing the alpha can help smooth it a little.
Comparison of default setting and with it set to the same color as selected faces:

 

Note that this value also affects active vertices and edges as well as faces.